Tessera
it'sd been a while since I've done tech work but if your pre is self/auto biasing, perhaps the plate voltage is too high. This could happen during start up only... or continue during operation. Though not at every turn on.... which would explain the makers statement that they found nothing wrong. Intermittent issues are the worst to figure out, ...if of course, this is the thing. running too hot sure would explain the shortened life expectancy though.
Another thought is the common thread note... as both the line stage and phono stage experience the same issues, ultimately, looking at what is common to both seems in order... output stage breakdown could be asking for a greater signal magnitude and create a higher continuous voltage through the input stages. Grounds or shorts and even poor connections, or those who have broken down over time, will cause such things.
have you had to raise the vol level more so as time has passed than you did originally??
It's obvious they've missed something... give them another crack at it on their dime this go 'round.
I'd also start fresh by asking what they've determined is average tube life with this unit?
Prior to or surely thereafter a decision to fix or replace is on the horizon... or stock up on tubes!